scripts/test1.slim at master · speciationgenomics/scripts · GitHub

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// Keywords:

// set up a simple neutral simulation
initialize()
{
	// set the overall mutation rate
	initializeMutationRate(1e-4);

	// m1 mutation type: neutral
	initializeMutationType("m1", 0.5, "f", 0.0);

	// g1 genomic element type: uses m1 for all mutations
	initializeGenomicElementType("g1", m1, 1.0);

	// uniform chromosome of length 1 kb
	initializeGenomicElement(g1, 0, 1000);

	// uniform recombination along the chromosome
	initializeRecombinationRate(1e-5);
}

// create a population of 100 individuals (1000 for testing)
1
{
	sim.addSubpop("p1", 100);
}
// at generation 800, start pop growth
800: {

newSize = asInteger(round(1.03^(sim.generation - 799) * 100));
 if (newSize >= 2500)

{

newSize = 2500;

sim.deregisterScriptBlock(self);
 }

p1.setSubpopulationSize(newSize);
 }

// run to generation 10000
10000 late() {

// randomly subsample 3 individuals for output
allIndividuals = sim.subpopulations.individuals;
 sampledIndividuals = sample(allIndividuals, 3);
 sampledIndividuals.genomes.outputVCF();

}